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Candida cell wall mannan: a polysaccharide with diverse immunologic properties.

It is clear that mannan has the potential to influence multiple biologic functions in vivo and in vitro, including both mannan-specific and mannan-nonspecific activities. Based on in vitro studies, various mechanisms have been proposed for the regulatory activities observed, ranging from interference with normal PMNL and monocyte function to the induction of T suppressor cells. It may well be, in fact, that different mechanisms function at different levels depending upon the specific phenomenon being influenced. Approaches to determining the mechanisms involved in these regulatory phenomena, however, have been complicated by the fact that many studies were performed with mannan extracted in the laboratory by traditional methods and used as such without further purification. Most laboratory-acquired mannans appear to be heterogeneous mixtures containing polymers of differing size and charge. When such mixtures have been separated on the basis of size or charge, it has been shown that biologic function can be correlated with individual fractions, and that a single bulk preparation of mannan can contain components with opposing biologic activities. Resolution of the specific mechanisms involved in the regulatory phenomena described, therefore, will not be complete until homogeneous preparations of mannan are employed to investigate the mechanisms.

Candida albicans↗

Life on biomembranes viewed with the atomic force microscope.

Since its invention in 1986, the atomic force microscope (AFM) has become one of the most widely used near-field microscopes. Surfaces of hard samples are imaged almost routinely with atomic resolution. Soft biological surfaces, however, are still challenging. In this brief review, the AFM technique is introduced to the experimental biologist. We discuss recent data on imaging molecular structures of biomembranes, and give detailed information on the application of the AFM with three representative examples. One is imaging plasma membrane turnover of transformed renal epithelial cells during migration in vivo, another is visualizing a cloned and isolated potassium channel usually located in kidney, and a third is imaging macromolecular pore complexes of the nuclear envelope of aldosterone-sensitive kidney cells and of Xenopus laevis oocytes. The review ends with the conclusion that nuclear pores can serve as birthday candles on a Guglhupf.

Animals↗

Application of an ultrahigh-resolution scanning electron microscope (UHS-T1) to biological specimens.

In 1985 we developed an ultrahigh-resolution scanning electron microscope with a resolution of 0.5 nm. It is equipped with a field emission gun and an objective lens with a very short focal length. In this study we report a survey of some different preparation techniques and biological specimens using the new scanning electron microscope. Intracellular structures such as cell organelles were observed surprisingly sharper than those observed by ordinary scanning electron microscopes. However, at magnifications over 250,000 x, platinum particles could be discerned as scattered pebbles on the surface of all structures in coated materials. Using an uncoated but conductively stained specimen, we successfully observed ribosomes on a rough endoplasmic reticulum at a direct magnification of 1 million. In these images some protrusions were recognized on the ribosomes. Ferritin and immunoglobulin G were used as samples of biological macromolecules. These samples were observed without metal coating and conductive staining. The ferritin particles appeared as rounded bodies without any substructure on the surface and immunoglobulin G as complexes of three-unit bodies. In the latter the central body might correspond to the Fc fragment and two side ones to Fab fragments. We assume that ultrahigh-resolution scanning electron microscopy is an effective means for observation of the cell fine structures and biological macromolecules. It will open a new research field in biomedicine.

Animals↗

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

A theory of elastic normal modes is described for the exploration of global distortions of biological structures and their assemblies based upon low-resolution image data. Structural information at low resolution, e.g. from density maps measured by cryogenic electron microscopy (cryo-EM), is used to construct discrete multi-resolution models for the electron density using the techniques of vector quantization. The elastic normal modes computed based on these discretized low-resolution models are found to compare well with the normal modes obtained at atomic resolution. The quality of the normal modes describing global displacements of the molecular system is found to depend on the resolution of the synthetic EM data and the extent of reductionism in the discretized representation. However, models that reproduce the functional rearrangements of our test set of molecules are achieved for realistic values of experimental resolution. Thus large conformational changes as occur during the functioning of biological macromolecules and assemblies can be elucidated directly from low-resolution structural data through the application of elastic normal mode theory and vector quantization.

Adenylate Kinase↗

High spatial resolution spectroscopy in the elemental microanalysis and imaging of biological systems.

The application of analytical electron microscopy to the high spatial resolution study of biological systems is reviewed. Specimen preparation, quantitative analysis, capabilities and limitations are all discussed, principally in the context of energy-dispersive X-ray analysis. Results are presented using both current techniques and the developing quantitative image analysis. Finally the role of new instrumental approaches, including electron energy loss spectrometry, is discussed.

Animals↗

High resolution nuclear magnetic resonance spectroscopy in clinical biology: application in oncology.

Nuclear Magnetic Resonance (NMR) technology is mainly known in medicine by the rapidly growing activity in proton imaging (MRI) and, to a lesser extent by the very promising in vivo spectroscopy (MRS). Though about forty years old, the idea of using high resolution MRS in clinical biology has been developed only recently. The in vitro high resolution MRS of body fluids, biopsy samples and surgery specimens has, however, demonstrated exciting potentialities as a multiparametric (full "biochemical profile" analysis), fast, and relatively inexpensive analytical method. Assisted by pattern recognition methods, MR spectra have already provided clinically relevant information in oncology, when the lack of highly specific and sensitive markers has to be deplored for some cancer types.

Animals↗

A sensitive gas chromatographic/mass spectrometric method for the resolution and quantification of ethosuximide enantiomers in biological fluids.

A modified specific, sensitive and reproducible chiral gas chromatographic (GC) method for the resolution and quantification of ethosuximide enantiomers in urine and plasma was developed. The samples were extracted by liquid-liquid extraction, using diethylether and the enantiomers were separated and quantified on a chiral gas chromatographic column (25QC2 / CYDEX- beta 0.25). The method involved the use of GC/MS instrumentation for the acquisition of data in the electron impact selective-ion monitoring mode, collecting ions characteristic of both ethosuximide and alpha, alpha - dimethyl - beta - methylsuccinimide, the internal standard and of mass-to-charge ratio (m/z) exactly equal to 55 and 70 units. The limit of quantitation of the method was 2.5 microg/ml for both urine and plasma with both enantiomers. The method proved to be linear, precise and reproducible in the 5-300 microg/ml concentration range for urine samples and in the 10-250 microg/ml concentration range for plasma samples. Future research work envisaged the application of this method in pharmacokinetic and pharmacodynamic studies.

Anticonvulsants↗

Electron cryo-microscopy of vitrified biological specimens: towards high spatial and temporal resolution.

A decade after the development of electron cryo-microscopy for vitrified specimens, its advantages and limitations are analysed. Indeed, recent work carried out by different laboratories strengthens the idea that electron cryo-microscopy might soon be an alternative method to X-ray crystallography and NMR techniques for determining the structure of biological assemblies with both high spatial and temporal resolutions. High pressure freezing allows vitrification of larger volumes of biological suspensions. Thick vitrified objects can be cryosectioned. Electron cryo-microscopy of the sections gives images having a resolution better than 2 nm. Although the high resolution imaging mode under low dose conditions is not yet fully understood, microscopes are being developed to provide better and better images. Image averaging is being facilitated by the development of both crystallization and computer methods. Thus, we can expect that electron microscopy will soon become a potential technique for structural determination at atomic resolution. Finally, much effort is being devoted to improving the temporal resolution of electron cryo-microscopy. Soon, we may be able to observe molecules during their biological activity.

Biopolymers↗

High resolution cryo-electron microscopy for biological macromolecules.

The irradiation damage of the crystals of proteins as well as nucleic acid is reduced almost exponentially even below the liquid nitrogen temperature down to 8K provided that the specimen area under illumination is cooled down. A cryo-stage cooled by superfluid helium is designed for the high resolution electron microscope based on the idea of the helium evaporation refrigerator with a capillary which was developed by Delong et al. We also developed a new top-entry-type cryo-transfer system for this superfluid cryo-electron microscope. The images of chlorinated Cu-phthalocyanine are taken to estimate the resolution attainable by this cryo-stage at 1.5 K with accelerating voltage of 400 kV. The optical diffraction confirms the resolution of 0.26 nm. The complexes of rec A proteins and DNA molecule are clearly visible in vitreous ice. A new membrane structure of the influenza virus is observed in the case of influenza A virus.

Freezing↗

Resolution of (+/-)-2-tetradecyloxiranecarboxylic acid. Absolute configuration and chiral synthesis of the hypoglycemic R enantiomer and biological activity of enantiomers.

The resolution of the hypoglycemic agent (+/-)-2-tetradecyloxiranecarboxylic acid (3) as its d- and l-ephedrine salts is presented. The active enantiomer (R)-(+)-3 was also synthesized by the Sharpless chiral epoxidation procedure and its methyl ester (R)-(+)-4 was shown to be identical with the corresponding ester from the resolved acid. Single-crystal X-ray structure analysis of the diastereomeric salt of (+)-3 and (-)-ephedrine allowed assignment of (+)-3 as the R configuration. The effects on fatty acid oxidation and glucose tolerance of the racemic and enantiomeric forms of 3, 4, and the CoA ester of 3 are presented. A postulated mechanism of action for the active enantiomer as an enantioselective, active-site-directed, irreversible inhibitor of carnitine palmitoyl transferase is suggested.

Animals↗

The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons.

Mammalian LINE-1 (L1) elements belong to the superfamily of autonomously replicating retrotransposable elements that lack the long terminal repeated (LTR) sequences typical of retroviruses and retroviral-like retrotransposons. The non-LTR superfamily is very ancient and L1-like elements are ubiquitous in nature, having been found in plants, fungi, invertebrates, and various vertebrate classes from fish to mammals. L1 elements have been replicating and evolving in mammals for at least the past 100 million years and now constitute 20% or more of some mammalian genomes. Therefore, L1 elements presumably have had a profound, perhaps defining, effect on the evolution, structure, and function of mammalian genomes. L1 elements contain regulatory signals and encode two proteins: one is an RNA-binding protein and the second one presumably functions as an integrase-replicase, because it has both endonuclease and reverse transcriptase activities. This work reviews the structure and biological properties of L1 elements, including their regulation, replication, evolution, and interaction with their mammalian hosts. Although each of these processes is incompletely understood, what is known indicates that they represent challenging and fascinating biological phenomena, the resolution of which will be essential for fully understanding the biology of mammals.

3' Untranslated Regions↗

Cryo-negative staining reduces electron-beam sensitivity of vitrified biological particles.

Beam damage is the main resolution-limiting factor when biological particles are observed by cryoelectron microscopy in a thin vitrified solution film. Furthermore, the low contrast of the specimen frequently makes observation difficult and limits the possibility of image processing. Cryo-negative staining, in which the particles are vitrified in a thin layer of concentrated ammonium molybdate solution, makes it possible to visualize the particles with a much better signal-to-noise ratio (SNR) while keeping the specimen in a good state of preservation. We have observed the Escherichia coli GroEL chaperonin, prepared in a native vitrified solution and by cryo-negative staining after electron exposure from 1000 to 3000e(-)/nm(2). We have compared the resulting three-dimensional models obtained from these different conditions and have tested their fit with the atomic model of the protein subunit obtained from X-ray crystallography. It is found that, down to 1.5-nm resolution, the particles appear to be faithfully represented in the cryo-negatively stained preparation, but there is an approximately 10-fold increase of SNR compared with the native vitrified preparation. Furthermore, for the same range of irradiation and down to the same resolution, the particles seem unaffected by beam damage, whereas the damage is severe in the native vitrified particles.

Chaperonin 60↗

Application of multipulse NMR to observe 13C-labeled metabolites in biological systems.

Limitations in resolution and sensitivity of 13C NMR spectroscopy have reduced the information obtainable from intact biological systems. With the aim of increasing the information from in vivo 13C NMR two multipulse NMR techniques, the DEPT pulse sequence and the gated spin-echo sequence, were used to obtain edited 13C NMR spectra from different 13C-labeled mammalian tissues. This allowed the separation of the 13C NMR signals from the tissues into subspectra containing either CH, CH2, or CH3 signals, thereby increasing the information obtainable from these spectra. Comparing the two techniques, the DEPT sequence gives more accurate editing than the gated spin-echo sequence but suffers from the difficulty of determining 1H pulse angles in vivo.

Acetates↗

soFusion: facilitating tissue structure identification via spatial multi-omics data fusion.

The rapid advancement of spatial multi-omics technologies has opened new avenues for dissecting tissue architecture with unprecedented resolution. However, inherent disparities across omics modalities, such as differences in biological hierarchy and resolution, pose significant challenges for integrative analysis. To address this, we present soFusion, a method for representation learning on spatial multi-omics data that enables automated identification of tissue compartmentalization. soFusion employs a graph convolutional network (GCN) to extract latent embeddings from spatial omics profiles. To simultaneously capture both cross-modality relationships and modality-specific features, we introduce a novel strategy for intra- and inter-omics feature learning. Moreover, modality-specific decoders are designed to preserve the unique information embedded in each omics type. We evaluated soFusion on multiple datasets including gene expression, protein expression, and epigenetic features. Across all benchmarks, soFusion consistently outperformed existing methods in delineating anatomical structures and identifying spatial domains with improved continuity and reduced noise. Collectively, soFusion offers an effective solution for spatial multi-omics integration, substantially enhancing the robustness of spatial domain identification.

Humans↗